Re: [Freesurfer] xhemi

When creating a laterality-free atlas one needs to make sure to do the same thing to the left and right hemi. Eg, the mni152 is not laterally symmetric, so you will get a different registration when you register your volume directly to the mni152 vs left-right reversing your volume and then reg

Re: [Freesurfer] xhemi

External Email - Use Caution Dear Doug, Thanks. A regional Laterality Index can be calculated using XHEMI (as described on the wiki) but also in a different way, e.g. using the default FS output from ?h*.stats files and e.g. doing (LH-RH)/((LH+RH)/2) or some other formula. You onc

Re: [Freesurfer] xhemi

Yes, they are. BTW, you should not need to mri_convert the thickness to mgh format On 11/27/2023 10:01 AM, Joost Janssen wrote: External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The fol

[Freesurfer] xhemi

External Email - Use Caution Dear Doug, The objective is to have _regional_ laterality index for thickness for aparc mapped to the left hemisphere. The following commands work without error but are they correct for meeting my objective? Thanks. surfreg --s $subject --t fsaverage_

Re: [Freesurfer] xhemi Longitudinal Comparison {Disarmed}

, April 19, 2019 12:57 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] xhemi Longitudinal Comparison == CAUTION: External Sender == This message came from outside of Penn State Health & College of Medicine. Please use caution when opening attachments or links. On 4/19/2019 11:3

Re: [Freesurfer] xhemi Longitudinal Comparison

On 4/19/2019 11:35 AM, Wang, Xiaoyu wrote: External Email - Use Caution Dear FreeSurfer Experts, We are trying to compare the early onset hemisphere vs Late onset hemisphere of PD patients. I am trying to use Xhemi in order to reorganize all early onset hemisphere to the left hemi

[Freesurfer] xhemi Longitudinal Comparison

External Email - Use Caution Dear FreeSurfer Experts, We are trying to compare the early onset hemisphere vs Late onset hemisphere of PD patients. I am trying to use Xhemi in order to reorganize all early onset hemisphere to the left hemisphere and the late onset to the right

Re: [Freesurfer] xhemi label

copy it to $FREESURFER_HOME/bin and then chmod a+x mris_apply_reg then rehash On 3/21/17 8:23 AM, Marissa Pifer wrote: Hi Doug, I'm not sure how to use this binary. Do I need to install it? Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> wrot

Re: [Freesurfer] xhemi label

Hi Doug, I'm not sure how to use this binary. Do I need to install it? Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve wrote: > Are you using v5.3? You will need a version 6. You can get this binary > for v6 here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > >

Re: [Freesurfer] xhemi label

Yes I am using 5.3. Thank you! Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve wrote: > Are you using v5.3? You will need a version 6. You can get this binary > for v6 here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > > > On 03/17/2017 11:47 AM, Marissa Pifer

Re: [Freesurfer] xhemi label

Are you using v5.3? You will need a version 6. You can get this binary for v6 here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg On 03/17/2017 11:47 AM, Marissa Pifer wrote: > > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label > label/rh.V1_exvivo.thresh.label

Re: [Freesurfer] xhemi label

Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg ERROR: Option --src-label unknown On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve

Re: [Freesurfer] xhemi label

please send command line On 3/17/17 10:38 AM, Marissa Pifer wrote: Hi freesurfers, I am using xhemi to map the right hemisphere of each subject to the left hemisphere of the same subject. The first xhemi command works fine, but the 2nd step for mapping the label, I get this error: "Option -

[Freesurfer] xhemi label

Hi freesurfers, I am using xhemi to map the right hemisphere of each subject to the left hemisphere of the same subject. The first xhemi command works fine, but the 2nd step for mapping the label, I get this error: "Option --src-label unknown" Do you know how to fix this? Marissa ___

Re: [Freesurfer] xhemi final iteration

You will need a new version of make_average_surface, which you can get from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface make a back up of your current version, ie, cp $FREESURFER_HOME/bin/make_average_surface $FREESURFER_HOME/bin/make_average_surface

Re: [Freesurfer] xhemi final iteration

Sorry about that, Outlook seems to be preventing me from sending the code in email. I have attached a text document of the output.  output Description: output ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

Re: [Freesurfer] xhemi final iteration

there's nothing there (?) On 05/14/2015 06:13 PM, Derek James Dean wrote: > Here is the debug output. > > > > ~$ cd $SUBJECTS_DIR > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fr

Re: [Freesurfer] xhemi final iteration

Here is the debug output.  ~$ cd $SUBJECTS_DIR ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addresse

Re: [Freesurfer] xhemi final iteration

can you run it with --debug as the first option and send the terminal output? On 05/14/2015 05:35 PM, Derek James Dean wrote: > > Hi Doug, > > Thanks for your help. > > When I run the following command: > images$ make_average_subject --out myatlas.i3 --surf-reg > myatlas.i2.sphere.reg --fsgd lat

Re: [Freesurfer] xhemi final iteration

Hi Doug, Thanks for your help. When I run the following command: images$ make_average_subject --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --fsgd laterality.fsgd --xhemi --lh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr

Re: [Freesurfer] xhemi final iteration

Use --lh instead of --hemi lh On 05/10/2015 03:32 PM, Derek James Dean wrote: > Dear Freesurfer community, > > I am trying to complete the final iteration described in the Xhemi > wiki page to compare left-right hemisphere symmetry between a patient > and control group but I get an error when I

[Freesurfer] xhemi final iteration

Dear Freesurfer community, I am trying to complete the final iteration described in the Xhemi wiki page to compare left-right hemisphere symmetry between a patient and control group but I get an error when I run make_average_subject. Basic information: FREESURFER_HOME: /projects/ics/software/freesu

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

OK, you're using an older version that did not copy the volume. You can just do this cp subject/surf/lh.volume subject/surf/rh.volume Note the change from lh to rh! doug On 04/28/2014 06:25 PM, Yizhou Ma wrote: > Thanks Doug. I don't see an error message in xhemireg.?h.log files. > Please s

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

Hi Doug, I just read from the .log files that the lh.thickness/area/pial/... files in subject/xhemi/surf are copied from subject/surf at the end of the command. Thus it seems that I can just copy lh.volume, too? Thanks, Cherry On Mon, Apr 28, 2014 at 6:25 PM, Yizhou Ma wrote: > Thanks Doug. I

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

Thanks Doug. I don't see an error message in xhemireg.?h.log files. Please see attached for the files. On Mon, Apr 28, 2014 at 4:22 PM, Douglas N Greve wrote: > > Then something went wrong along the way. Check the xhemi/xhemireg.?h.log > to see if there is an error. If not, send the log file to

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

Then something went wrong along the way. Check the xhemi/xhemireg.?h.log to see if there is an error. If not, send the log file to me On 04/28/2014 04:14 PM, Yizhou Ma wrote: > Thanks Doug. I have ?h.volume in subject/surf but not in > subject/xhemi/surf. I followed this page > http://surfer.n

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

Thanks Doug. I have ?h.volume in subject/surf but not in subject/xhemi/surf. I followed this page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi and I think it is a problem with surfreg rather than mris_preproc. Can I just copy the ?h.volume from subject/surf to subject/xhemi/surf? Best, Cherry

Re: [Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

There should be a ?h.volume file. Are you sure there is not? You can specify -meas volume when you run mris_preproc doug On 04/27/2014 08:35 PM, Yizhou Ma wrote: > Dear freesurfer experts, > > I am working on a project on cortical asymmetry and I have analyzed > vertex-wise cortical thickness/

[Freesurfer] Xhemi: vertex-wise volume asymmetry analysis?

Dear freesurfer experts, I am working on a project on cortical asymmetry and I have analyzed vertex-wise cortical thickness/surface area asymmetry. However, I noticed that Freesurfer doesn't not seem to facilitate such analysis for gray matter volume, as after running surfreg -xhemi there is no ?h

Re: [Freesurfer] xhemi - xhemireg file

sorry, try now On 01/28/2014 11:26 AM, Adam Martersteck wrote: > > Hi Freesurfer team, > > I noticed that the xhemireg file is missing from: > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg > > I’m assuming the xhemireg for v5.3.0 (found in v5.3.0’s > $FS_HOME/bin/xhemi

[Freesurfer] xhemi - xhemireg file

Hi Freesurfer team, I noticed that the xhemireg file is missing from: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/xhemireg I'm assuming the xhemireg for v5.3.0 (found in v5.3.0's $FS_HOME/bin/xhemireg) is identical and I can use that with v5.1.0? Thanks, Adam ___

Re: [Freesurfer] xhemi correct for multiple comparisons

great thanks Doug! Is there any way to analyze group differences with xhemi? I can get the laterality indices per group, but I'd like to do a whole brain analyses looking at group differences in laterality indices. Thanks, Krista On Tue, Dec 10, 2013 at 2:01 PM, Douglas N Greve wrote: > > Yes,

Re: [Freesurfer] xhemi vertices

ay, January 8, 2014 9:11:04 PM > Subject: Re: [Freesurfer] xhemi vertices > > > To follow up, it is intended that you will map both hemispheres of a > given subject to one of the hemispheres of fsaverage_sym (it does not > matter which, but we usually use lh). You can then do

Re: [Freesurfer] xhemi vertices

To follow up, it is intended that you will map both hemispheres of a given subject to one of the hemispheres of fsaverage_sym (it does not matter which, but we usually use lh). You can then do the comparisons on that hemisphere. Does that make sense? doug On 01/08/2014 02:09 PM, Bruce Fischl

Re: [Freesurfer] xhemi vertices

Hi Sofie, no, they don't correspond. You need to use mri_surf2surf to map one to the other (which is a bit tricky). cheers Bruce On Wed, 8 Jan 2014, Sofie Valk wrote: > Dear Free Surfers, > > I have a short question regarding the mapping of vertices of the > fsaverage_sym, how do vertices in t

[Freesurfer] xhemi vertices

Dear Free Surfers, I have a short question regarding the mapping of vertices of the fsaverage_sym, how do vertices in the left hemisphere correspond to vertices in the right hemisphere? When I tested it, it did not seem that the first-indexed vertex on the left hemisphere corresponded to the

Re: [Freesurfer] xhemi installation

Try here instead ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/ On 12/18/2013 11:37 AM, Sofie Valk wrote: > Dear FreeSurfers, > > I have a question regarding the installation of xhemi (I am using FreeSurfer > 5.1) > > I tried to follow the guide on: > https://surfer.nmr.mgh.ha

[Freesurfer] xhemi installation

Dear FreeSurfers, I have a question regarding the installation of xhemi (I am using FreeSurfer 5.1) I tried to follow the guide on: https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi to install the necessary files, however the following files do not seem to be present on the ftpserver: ftp://sur

Re: [Freesurfer] xhemi correct for multiple comparisons

Yes, use the cache files. When "--cache" is used, the csdbase="cache" On 12/10/2013 12:20 PM, krista kelly wrote: > Hi again, > > I've looked into mri_glmfit-sim --help to figure out which files I > could overlay in tkurfer after correcting for multiple comparisons > using the instructions for

Re: [Freesurfer] xhemi correct for multiple comparisons

Hi again, I've looked into mri_glmfit-sim --help to figure out which files I could overlay in tkurfer after correcting for multiple comparisons using the instructions for xhemi on the freesurfer wiki. However, I do not see any of these files (csd.base...) in the glmdir/osgm folder. I only see ones

Re: [Freesurfer] xhemi correct for multiple comparisons

Great Thanks! On Mon, Dec 9, 2013 at 11:57 AM, Douglas N Greve wrote: > > On 12/09/2013 11:53 AM, krista kelly wrote: > > Thanks Doug! I'll try that instead. > > > > Also, do you or anyone else happen to have the answers to my other > > questions (reposted below): > > > > 1) When viewing the r

Re: [Freesurfer] xhemi correct for multiple comparisons

On 12/09/2013 11:53 AM, krista kelly wrote: > Thanks Doug! I'll try that instead. > > Also, do you or anyone else happen to have the answers to my other > questions (reposted below): > > 1) When viewing the results in tksurfer, which color represents "left > hemisphere is larger" and which repre

Re: [Freesurfer] xhemi correct for multiple comparisons

Thanks Doug! I'll try that instead. Also, do you or anyone else happen to have the answers to my other questions (reposted below): 1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is larger"? 2) I have no idea how

Re: [Freesurfer] xhemi correct for multiple comparisons

Run mris_preproc with --paired-diff-norm which will then compute LI = (L-R)/(.5*(L+R)) Note that some people use LI = (L-R)/(L+R) If that is what you want, then divide the mris_preproc result by 2 doug On 12/08/2013 08:45 PM, krista kelly wrote: > Hello, > > I'm analysing interhemispheric d

[Freesurfer] xhemi correct for multiple comparisons

Hello, I'm analysing interhemispheric differences using xhemi. I have followed the instructions on the webpage with no problems. I do have a few questions though. 1) When viewing the results in tksurfer, which color represents "left hemisphere is larger" and which represents "right hemisphere is

Re: [Freesurfer] Xhemi-Fsaverage Vs myatlas

I'm not sure I understand what you mean by that. Your inflated brain just needs to be inflated a little more to get the folds out of it. I cannot tell whether this is sufficient or not. I found that I had to iterate many times (on the order of 30) to get stable results. This is quite burdenso

Re: [Freesurfer] Xhemi question

, Daria From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, July 16, 2013 11:20 AM To: Boratyn, Daria A. Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Xhemi question Hi Daria, I'm not sure what you are trying to do. What do you

Re: [Freesurfer] Xhemi question

- From: Douglas N Greve mailto:gr...@nmr.mgh.harvard.edu>> Date: Fri, Jun 7, 2013 at 1:31 PM Subject: Re: [Freesurfer] Xhemi question To: Daria Boratyn mailto:bora...@nmr.mgh.harvard.edu>>, "Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>"

Re: [Freesurfer] Xhemi results

Thanks a lot! On Fri, Jul 12, 2013 at 6:58 PM, Douglas N Greve wrote: > It is the difference but it is on the tesselation of the left hemisphere. > If you want it on the right hemisphere, then you need to perform the > analysis on the right hemisphere. > doug > > > > On 07/12/2013 02:37 AM, amir

Re: [Freesurfer] Xhemi results

Is lh.lh-rh.thickness.sm00.mgh the left hemisphere overlay or the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? I need to see the difference map of left and right (lh-rh) overlaid on both hemispheres! On Thu, Jul 11, 2013 at 6:01 PM, Douglas

Re: [Freesurfer] Xhemi results

As I mentioned before in my second question : tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh tksurfer fsaverage_sym lh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh For Right and Left side! BR On Thu, Jul 11, 2013 at 4:38 PM, Douglas Greve wrote: > > I don'

Re: [Freesurfer] Xhemi results

I don't know what you mean by overlaying the results on L & R. What is your command line? On 7/11/13 3:34 AM, amirhossein manzouri wrote: Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR

Re: [Freesurfer] Xhemi results

Thanks Doug, When I overlay the results on L & R , I see different patterns on each hemisphere. Is it something that I don't understand correctly? BR On Wed, Jul 10, 2013 at 5:45 PM, Douglas N Greve wrote: > > On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > > Dear Doug and FS experts, > >

Re: [Freesurfer] Xhemi results

On 07/10/2013 01:26 AM, amirhossein manzouri wrote: > Dear Doug and FS experts, > I am trying to use Xhemi tool to study asymmetry in the brain. I have > done the exact procedure you mentioned in WiKi for a group of 40 controls. > 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical

[Freesurfer] Xhemi results

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of eac

[Freesurfer] Xhemi results

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of eac

Re: [Freesurfer] Xhemi files can not be downloaded

Hi Hamza, try mri_convert.mac doug On 07/03/2013 07:27 AM, Hamza Alshuft wrote: > Thanks for the help > Unfortunately after your reply I could only > downloadftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc > the rest of the files are still un-downloadable! > > I have

Re: [Freesurfer] Xhemi files can not be downloaded

Thanks for the help Unfortunately after your reply I could only download ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc the rest of the files are still un-downloadable! I have Mac freesurfer v5.1 and use "curl –O ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/f

Re: [Freesurfer] Xhemi files can not be downloaded

ok, try now On 07/02/2013 06:53 AM, Hamza Alshuft wrote: > Dear Freesurfer experts > > I can not download files required for surface based inter hemispheric > registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome > "curl: (78) RETR response: 550" > I am currently using Mac version 5

[Freesurfer] Xhemi files can not be downloaded

Dear Freesurfer experts I can not download files required for surface based inter hemispheric registration :http://ftp.nmr.mgh.harvard.edu/fswiki/Xhemi outcome "curl: (78) RETR response: 550" I am currently using Mac version 5.1. Any help please? Thanks, Hamza This message and any attachmen

Re: [Freesurfer] Xhemi question

Hi Daria, I would smooth the left and right separately, then compute the LI. doug On 07/01/2013 01:14 PM, Boratyn, Daria A. wrote: > Hi Doug, > > Could you please clarify when you suggest it's best to smooth if using the > xhemi scripts? I'm a bit confused based on the emails below. > http://www

Re: [Freesurfer] Xhemi question

Hi Doug, Could you please clarify when you suggest it's best to smooth if using the xhemi scripts? I'm a bit confused based on the emails below. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg27761.html Thank you, Daria From: Douglas N Gr

Re: [Freesurfer] Xhemi question

Hi Daria, this is not something you would do with tkregister. First, you need to map the curvature from the individual subject to fsaverage_sym. You can do this for all subjects in your group with a call to mris_preproc; spec --meas curv instead of --meas thickness. Then load this as an overla

Re: [Freesurfer] Xhemi question

Hi Doug, I've tried using tkregister2 and registering my individual subject's T1 to the fsaverage_sym but it hasn't worked. Could you point me to the correct movable volume and register.dat files that I should use? I'm not sure what they print out as. Thank you, Daria ___

Re: [Freesurfer] Xhemi question

Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding x

Re: [Freesurfer] Xhemi stat questions

If you use thick = fast_vol2mat(MRIread('file.mgh')); thick will be a matrix of nsubjects-by-nvertices. Note that the vertex indices from labels are 0-based whereas matlab expects 1-based. doug On 03/27/2013 09:08 AM, Gabriel Gonzalez Escamilla wrote: > That makes much more sense than the th

Re: [Freesurfer] Xhemi stat questions

That makes much more sense than the thing I was looking for.Now I have a problem reading the lh.lh-rh.thickness.mgh with the load_mgh.m function, as I have no idea of how to read it to get the vertex by vertex thickness value of each subject.I tryed as [thick, ~,~,~]=load_mgh('file.mgh',[],[1:nSubj

Re: [Freesurfer] Xhemi stat questions

Unless you specifically need them for an individual, you should get them from lh.lh-rh.thickness.mgh because that data is sampled onto the symmetric template and so should be unbiased (ie, it will not systematically favor lh or rh). doug On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote

Re: [Freesurfer] Xhemi stat questions

Dear Doug,I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals?I suppose that I should read the lh.lh-rh.thickn

Re: [Freesurfer] Xhemi stat questions

I mean of a given subject, I suppose that on the fsaverage_sym, I would read the lh.lh-rh.thickness.mgh. But, As I'm thinking about this, I'm wondering if it has sense, or if I should obtain the lh-rh thickness differences? Nevertheless, I have no idea how to get any of those measurements.Regards,G

Re: [Freesurfer] Xhemi stat questions

Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym? doug On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: > Thank you, so I'm keeping the one I had. > > Sorry for my bad explanation. When I do a normal cortical thickness >

Re: [Freesurfer] Xhemi stat questions

Thank you, so I'm keeping the one I had.Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible

Re: [Freesurfer] Xhemi stat questions

On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: > Thanks a lot for your answer, > > I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. > > When I wrote CT, I was meaning cortical thickness, as normally this

Re: [Freesurfer] Xhemi stat questions

Thanks a lot for your answer,I'm sending you attached the diff of the two mris_preproc.When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indi

Re: [Freesurfer] Xhemi stat questions

On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: > Dear Doug, > > I've seen that you restore the files to download, for the Xhemi > registration. While I'm checking for the statistical process, I've > seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: > 1.59.2.4, and the

[Freesurfer] Xhemi stat questions

Dear Doug,I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.6

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

It is actually there. I changed the location but did not update the wiki. Look in this dir ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ xhemi-reg On 3/14/13 7:43 PM, Negar Memarian wrote: Dear Doug, Fol

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

Dear Doug, Following up on my yesterday email, I would appreciate if you kindly upload the following files (required for Xhemi) so the ftp download will be possible. I am currently using version 5.1 of FreeSurfer and need the installation of these files in order to be able to run the Xhemi process

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

Hi Doug, No, I'm using 5.1. I'd appreciate if you copy them back. Thank you, Negar On Wed, Mar 13, 2013 at 2:50 PM, Douglas Greve wrote: > Oh, sorry, those get periodically deleted. Are you using 5.2? If so they > are already in the distribution. If not, I'll copy them back over. > doug > > >

Re: [Freesurfer] Xhemi files do not exist in the specified ftp location

Oh, sorry, those get periodically deleted. Are you using 5.2? If so they are already in the distribution. If not, I'll copy them back over. doug On 3/13/13 10:33 PM, Negar Memarian wrote: > Dear Doug, > Can you please advise me of the correct location of the ftp > directories/files required to

[Freesurfer] Xhemi files do not exist in the specified ftp location

Dear Doug, Can you please advise me of the correct location of the ftp directories/files required to be installed for surface based interhemispheric registration? I'm trying to download and install the required files from the specified path: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/

Re: [Freesurfer] Xhemi questions

mc-z is a simulation that replaces the data with smoothed gaussian noise. permutation uses your data and changes the order of the rows in the design matrix. If the noise in your data set is Gaussian, they will give the same result (in theory:). If the noise is not gaussian, then the mc-z will

Re: [Freesurfer] Xhemi questions

Thanks you for your quick answer Doug,Just one clarification, in the correction for multiple comparisons, which is the main difference between the mc-z and the permutation test? rather than making simultaions or working on original data. And Why is 5000 runs recommended to mc-z and 1 for permut

Re: [Freesurfer] Xhemi questions

On 02/06/2013 12:49 PM, Gabriel Gonzalez Escamilla wrote: > Dear Doug and FreeSurfer experts, > > Thnak you so much for all your lasts responses!. > > I did ran succesfully all the pre-processing for the interhemispheric > comparisons on FS. Now I have a couple questions: > > given the command fo

[Freesurfer] Xhemi questions

Dear Doug and FreeSurfer experts,Thnak you so much for all your lasts responses!.I did ran succesfully all the pre-processing for the interhemispheric comparisons on FS. Now I have a couple questions:given the command for interhemispheric comparisons:mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glm

Re: [Freesurfer] xhemi problem

Thanks Doug for your answerBut, always the first one ends properlysurfreg --s c_003 --t fsaverage_sym --lhit's the second one that have two different errors:surfreg --s c_003 --t fsaverage_sym --lh --xhemiAnd yes you are right, it says that it's because of the library but, the original mri_convert

Re: [Freesurfer] xhemi problem

The second command is probably failing because the first command is failing. The 1st is failing because you don't have GLIBC 2.4. I'll have to leave that one for Nick or Zeke. doug On 01/26/2013 03:21 PM, Gabriel Gonzalez Escamilla wrote: > Well there is actually two kinds of error: > > 1) when

Re: [Freesurfer] xhemi problem

Well there is actually two kinds of error:1) when I run surfreg --s c_003 --t fsaverage_sym --lhand then:surfreg --s c_003 --t fsaverage_sym --lh --xhemi sáb ene 26 21:09:21 CET 2013 setenv SUBJECTS_DIR /root/trabajo/freesurfer/subjects cd /root /root/trabajo/freesurfer/bin/surfreg --s c_003 --t f

Re: [Freesurfer] xhemi problem

Can you send the command line and terminal output? On 01/25/2013 09:38 AM, Gabriel Gonzalez Escamilla wrote: > Dear FS experts, > > I'm trying to perform the intrerhemispheric registration method on my > centOS 4, I have downloaded all the files, but the mri_convert is > saying that does not fo

[Freesurfer] xhemi problem

Dear FS experts,I'm trying to perform the intrerhemispheric registration method on my centOS 4, I have downloaded all the files, but the mri_convert is saying that does not found the necessary libraries. I did download the mri_convert.linux, I have tried to re-download the file, but it apparentelly